References Associated with Literature Topic: Computational analysis Help


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Wang X, et al.  (2012) Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PLoS Comput Biol 8(6):e1002566
Wang Y, et al.  (2012) Interrogating noise in protein sequences from the perspective of protein-protein interactions prediction. J Theor Biol 315():64-70
Wen Z, et al.  (2012) Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle. PLoS One 7(7):e41854
Wereszczynski J and McCammon JA  (2012) Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations. Proc Natl Acad Sci U S A 109(20):7759-64
Witten DM and Noble WS  (2012) On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Res 40(9):3849-55
Wong AK, et al.  (2012) IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res 40(Web Server issue):W484-90
Wong H, et al.  (2012) A predictive computational model of the dynamic 3D interphase yeast nucleus. Curr Biol 22(20):1881-90
Wu M and Chan C  (2012) Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data. Brief Bioinform 13(2):150-61
Wu M, et al.  (2012) Identification of drug targets by chemogenomic and metabolomic profiling in yeast. Pharmacogenet Genomics 22(12):877-86
Wuttke D, et al.  (2012) Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PLoS Genet 8(8):e1002834
Wyrick JJ  (2012) Computational analysis of promoter elements and chromatin features in yeast. Methods Mol Biol 809():217-35
Xia T, et al.  (2012) Network motif comparison rationalizes Sec1/Munc18-SNARE regulation mechanism in exocytosis. BMC Syst Biol 6(1):19
Xie P  (2012) A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases. Proteins 80(8):2020-34
Yan L, et al.  (2012) Dose-response aligned circuits in signaling systems. PLoS One 7(4):e34727
Yang H, et al.  (2012) Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. Bioinformatics 28(10):1383-9
Yang Z and Sankoff D  (2012) Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. BMC Bioinformatics 13 Suppl 9():S8
Yao F, et al.  (2012) Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets. BMC Bioinformatics 13():24
Yeh CY, et al.  (2012) Pathway detection from protein interaction networks and gene expression data using color-coding methods and A * search algorithms. ScientificWorldJournal 2012():315797
Yoshidome T, et al.  (2012) Structural characteristics of yeast F(1)-ATPase before and after 16-degree rotation of the gamma subunit: Theoretical analysis focused on the water-entropy effect. J Chem Phys 137(3):035102
Young TR, et al.  (2012) Clustering in cell cycle dynamics with general response/signaling feedback. J Theor Biol 292():103-15
Yu G, et al.  (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16(5):284-7
Yu Q, et al.  (2012) MOfinder: A Novel Algorithm for Detecting Overlapping Modules from Protein-Protein Interaction Network. J Biomed Biotechnol 2012():103702
Yun Y, et al.  (2012) A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs. Genome Res 22(6):1089-97
Zamir L, et al.  (2012) Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility. Proc Natl Acad Sci U S A 109(7):E406-14
Zaugg JB and Luscombe NM  (2012) A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res 22(1):84-94
Zechner C, et al.  (2012) Moment-based inference predicts bimodality in transient gene expression. Proc Natl Acad Sci U S A 109(21):8340-5
Zeng T and Chen L  (2012) Tracing dynamic biological processes during phase transition. BMC Syst Biol 6 Suppl 1():S12
Zhang D, et al.  (2012) TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes. Bioinformatics 28(20):2696-7
Zhang J and Bao J  (2012) A modified method for calculating practical ethanol yield at high lignocellulosic solids content and high ethanol titer. Bioresour Technol 116():74-9
Zhang Q, et al.  (2012) A model-based method for gene dependency measurement. PLoS One 7(7):e40918